src

residue.cpp File Reference

Handle macromolecule residues. More...

#include "babelconfig.h"
#include <iostream>
#include <fstream>
#include "mol.h"
#include "bitvec.h"

Namespaces

namespace  OpenBabel
namespace  OpenBabel::OBAminoAcidProperty
namespace  OpenBabel::OBResidueAtomProperty
namespace  OpenBabel::OBResidueIndex
namespace  OpenBabel::OBResidueProperty

Defines

#define MAXSETNO   40
#define MAXELEM   1024
#define MINELEM   29
#define MAXRES   100
#define MINRES   54
#define AA_ALA   (1<<1)
#define AA_GLY   (1<<2)
#define AA_LEU   (1<<3)
#define AA_SER   (1<<4)
#define AA_VAL   (1<<5)
#define AA_THR   (1<<6)
#define AA_LYS   (1<<7)
#define AA_ASP   (1<<8)
#define AA_ILE   (1<<9)
#define AA_ASN   (1<<10)
#define AA_GLU   (1<<11)
#define AA_PRO   (1<<12)
#define AA_ARG   (1<<13)
#define AA_PHE   (1<<14)
#define AA_GLN   (1<<15)
#define AA_TYR   (1<<16)
#define AA_HIS   (1<<17)
#define AA_CYS   (1<<18)
#define AA_MET   (1<<19)
#define AA_TRP   (1<<20)
#define IS_ACIDIC(x)   ((x) & ((AA_ASP)|(AA_GLU)))
#define IS_ACYCLIC(x)
#define IS_ALIPHATIC(x)
#define IS_AROMATIC(x)   ((x) & ((AA_HIS)|(AA_PHE)|(AA_TRP)|(AA_TYR)))
#define IS_BASIC(x)   ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS)))
#define IS_BURIED(x)
#define IS_CHARGED(x)
#define IS_CYCLIC(x)
#define IS_HYDROPHOBIC(x)
#define IS_LARGE(x)
#define IS_MEDIUM(x)
#define IS_NEGATIVE(x)   ((x) & ((AA_ASP)|(AA_GLU)))
#define IS_NEUTRAL(x)
#define IS_POLAR(x)
#define IS_POSITIVE(x)   ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS)))
#define IS_SMALL(x)   ((x) & ((AA_ALA)|(AA_GLY)|(AA_SER)))
#define IS_SURFACE(x)

Functions

static unsigned int GetAtomIDNumber (const char *atomid)
static unsigned int GetResidueNumber (const char *res)
static void SetResidueKeys (const char *residue, unsigned int &reskey, unsigned int &aakey)

Variables

static const unsigned int ACIDIC = 0
static const unsigned int ACYCLIC = 1
static const unsigned int ALIPHATIC = 2
static const unsigned int AROMATIC = 3
static const unsigned int BASIC = 4
static const unsigned int BURIED = 5
static const unsigned int CHARGED = 6
static const unsigned int CYCLIC = 7
static const unsigned int HYDROPHOBIC = 8
static const unsigned int LARGE = 9
static const unsigned int MEDIUM = 10
static const unsigned int NEGATIVE = 11
static const unsigned int NEUTRAL = 12
static const unsigned int POLAR = 13
static const unsigned int POSITIVE = 14
static const unsigned int SMALL = 15
static const unsigned int SURFACE = 16
static const unsigned int ALPHA_CARBON = 0
static const unsigned int AMINO_BACKBONE = 1
static const unsigned int BACKBONE = 2
static const unsigned int CYSTEINE_SULPHUR = 3
static const unsigned int LIGAND = 4
static const unsigned int NUCLEIC_BACKBONE = 5
static const unsigned int SHAPELY_BACKBONE = 6
static const unsigned int SHAPELY_SPECIAL = 7
static const unsigned int SIDECHAIN = 8
static const unsigned int SUGAR_PHOSPHATE = 9
static const unsigned int ALA = 0
static const unsigned int GLY = 1
static const unsigned int LEU = 2
static const unsigned int SER = 3
static const unsigned int VAL = 4
static const unsigned int THR = 5
static const unsigned int LYS = 6
static const unsigned int ASP = 7
static const unsigned int ILE = 8
static const unsigned int ASN = 9
static const unsigned int GLU = 10
static const unsigned int PRO = 11
static const unsigned int ARG = 12
static const unsigned int PHE = 13
static const unsigned int GLN = 14
static const unsigned int TYR = 15
static const unsigned int HIS = 16
static const unsigned int CYS = 17
static const unsigned int MET = 18
static const unsigned int TRP = 19
static const unsigned int ASX = 20
static const unsigned int GLX = 21
static const unsigned int PCA = 22
static const unsigned int HYP = 23
static const unsigned int A = 24
static const unsigned int C = 25
static const unsigned int G = 26
static const unsigned int T = 27
static const unsigned int U = 28
static const unsigned int UPLUS = 29
static const unsigned int I = 30
static const unsigned int OMC = 33
static const unsigned int M2G = 36
static const unsigned int OMG = 38
static const unsigned int YG = 39
static const unsigned int H2U = 40
static const unsigned int PSU = 42
static const unsigned int UNK = 43
static const unsigned int ACE = 44
static const unsigned int FOR = 45
static const unsigned int HOH = 46
static const unsigned int DOD = 47
static const unsigned int SO4 = 48
static const unsigned int PO4 = 49
static const unsigned int NAD = 50
static const unsigned int COA = 51
static const unsigned int NAP = 52
static const unsigned int NDP = 53
static const unsigned int AMINO = 0
static const unsigned int AMINO_NUCLEO = 1
static const unsigned int COENZYME = 2
static const unsigned int ION = 3
static const unsigned int NUCLEO = 4
static const unsigned int PROTEIN = 5
static const unsigned int PURINE = 6
static const unsigned int PYRIMIDINE = 7
static const unsigned int SOLVENT = 8
static const unsigned int WATER = 9
static char Residue [MAXRES][4]
static char ElemDesc [MAXELEM][4]
static unsigned int ResNo = MINRES
static unsigned int ElemNo = MINELEM

Detailed Description

Handle macromolecule residues.

Define Documentation

#define MAXSETNO   40

#define MAXELEM   1024

#define MINELEM   29

#define MAXRES   100

#define MINRES   54

#define AA_ALA   (1<<1)

#define AA_GLY   (1<<2)

#define AA_LEU   (1<<3)

#define AA_SER   (1<<4)

#define AA_VAL   (1<<5)

#define AA_THR   (1<<6)

#define AA_LYS   (1<<7)

#define AA_ASP   (1<<8)

#define AA_ILE   (1<<9)

#define AA_ASN   (1<<10)

#define AA_GLU   (1<<11)

#define AA_PRO   (1<<12)

#define AA_ARG   (1<<13)

#define AA_PHE   (1<<14)

#define AA_GLN   (1<<15)

#define AA_TYR   (1<<16)

#define AA_HIS   (1<<17)

#define AA_CYS   (1<<18)

#define AA_MET   (1<<19)

#define AA_TRP   (1<<20)

#define IS_ACIDIC ( x   )     ((x) & ((AA_ASP)|(AA_GLU)))

#define IS_ACYCLIC ( x   ) 

Value:

((x) & ((AA_ALA)|(AA_GLY)|(AA_LEU)|(AA_SER)| \
                                  (AA_VAL)|(AA_THR)|(AA_LYS)|(AA_ASP)| \
                                  (AA_ILE)|(AA_ASN)|(AA_GLU)|(AA_GLN)| \
                                  (AA_CYS)|(AA_MET)))

#define IS_ALIPHATIC ( x   ) 

Value:

((x) & ((AA_ALA)|(AA_GLY)|(AA_ILE)|(AA_LEU)| \
                                  (AA_VAL)))

#define IS_AROMATIC ( x   )     ((x) & ((AA_HIS)|(AA_PHE)|(AA_TRP)|(AA_TYR)))

#define IS_BASIC ( x   )     ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS)))

#define IS_BURIED ( x   ) 

Value:

((x) & ((AA_ALA)|(AA_CYS)|(AA_ILE)|(AA_LEU)| \
                                  (AA_MET)|(AA_PHE)|(AA_TRP)|(AA_VAL)))

#define IS_CHARGED ( x   ) 

Value:

((x) & ((AA_ASP)|(AA_GLU)|(AA_ARG)|(AA_HIS)| \
                                  (AA_LYS)))

#define IS_CYCLIC ( x   ) 

Value:

((x) & ((AA_HIS)|(AA_PHE)|(AA_PRO)|(AA_TRP)| \
                                  (AA_TYR)))

#define IS_HYDROPHOBIC ( x   ) 

Value:

((x) & ((AA_ALA)|(AA_LEU)|(AA_VAL)|(AA_ILE)| \
                                  (AA_PRO)|(AA_PHE)|(AA_MET)|(AA_TRP)))

#define IS_LARGE ( x   ) 

Value:

((x) & ((AA_ARG)|(AA_PHE)|(AA_GLN)|(AA_TYR)| \
                                  (AA_HIS)|(AA_LEU)|(AA_LYS)|(AA_ILE)| \
                                  (AA_GLU)|(AA_MET)|(AA_TRP)))

#define IS_MEDIUM ( x   ) 

Value:

((x) & ((AA_VAL)|(AA_THR)|(AA_ASP)|(AA_ASN)| \
                                  (AA_PRO)|(AA_CYS)))

#define IS_NEGATIVE ( x   )     ((x) & ((AA_ASP)|(AA_GLU)))

#define IS_NEUTRAL ( x   ) 

Value:

((x) & ((AA_ALA)|(AA_GLY)|(AA_LEU)|(AA_SER)| \
                                  (AA_VAL)|(AA_THR)|(AA_PHE)|(AA_GLN)| \
                                  (AA_TYR)|(AA_HIS)|(AA_CYS)|(AA_MET)| \
                                  (AA_TRP)|(AA_ILE)|(AA_ASN)|(AA_PRO)))

#define IS_POLAR ( x   ) 

Value:

((x) & ((AA_ASP)|(AA_ILE)|(AA_ASN)|(AA_GLU)| \
                                  (AA_SER)|(AA_THR)|(AA_ARG)|(AA_GLN)| \
                                  (AA_CYS)|(AA_HIS)))

#define IS_POSITIVE ( x   )     ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS)))

#define IS_SMALL ( x   )     ((x) & ((AA_ALA)|(AA_GLY)|(AA_SER)))

#define IS_SURFACE ( x   ) 

Value:

((x) & ((AA_THR)|(AA_LYS)|(AA_ASP)|(AA_ILE)| \
                                  (AA_ASN)|(AA_GLU)|(AA_PRO)|(AA_ARG)| \
                                  (AA_GLY)|(AA_SER)|(AA_GLN)|(AA_TYR)| \
                                  (AA_HIS)))